Purpose:Nuclear pore complexes are a large group of proteins responsible for molecular passages between the cytoplasm and the nucleus. We aimed to investigate the status of POM121 gene expression, which is one of the nuclear pore proteins in childhood acute leukemias, compared with the normal population, and its relationship with prognosis and other clinical findings. Methods:Fifty-nine patients with ALL and 21 patients with AML, followed up and treated between January 2008 and November 2013, and 36 control subjects were included in the study. A real-time PCR method was used to detect POM121 gene expressions. Results:The mean value of POM121 expression was 3.75±2.91 in ALL patients, 5.79±7.04 in AML patients, and 3.32±3.76 in the control group. POM121 expression was markedly higher in AML patients, but there was no statistically significant difference compared with the control group and ALL patients. Overall survival (OS) results were better in patients with lower POM121 expression than the mean of the control group among ALL and AML patients. However, the results were not statistically significant. Among ALL patients, patients with a higher POM121 expression than the mean of the control group, patients who had relapse and central nervous system involvement, patients who were in the standard risk group and without thrombocytopenia had statistically significantly lower OS results in the 3rd and 10th years. Conclusions:This is the first study in the literature to show the relationship between POM121 expression and prognosis in childhood leukemias, and this will be clarified further with more comprehensive studies.